Trapping A Better Mouse: Taxonomy of living organisms in SNOMED

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Trapping A Better Mouse Taxonomy of living
organisms in SNOMED

• Submitted byPenny Livesay BS, MA, DVM

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Proposal

• To organize SNOMED's taxonomy into a systematic
  and consistent Linnean hierarchy
• To remove all non-taxonomic information about
  living organisms from the taxonomic hierarchy
• To represent such information, when useful,
  reproducible, and retrievable, elsewhere in the
  nomenclaturefor instance, by qualifier values.

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Methods

• All existing taxonomic terms are being reviewed
  and standardized according to the Integrated
  Taxonomic Information System (ITIS). Where ITIS
  is not yet complete, the Smithsonian mammalian
  taxonomy website is being used as a secondary
  reference.
• All organisms will be represented by their
  scientific names as FSNs. Common names of
  organisms will be given as descriptions where
  appropriate.
• Will not attempt to represent all known organisms
  now, but will create a skeletal representation at
  least to the level of subfamilies for all
  families. Additional genera and species will be
  added as time allows or as requested by users.

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What is ITIS?

• A partnership of federal agencies formed to
  satisfy their mutual needs for scientifically
  credible taxonomic information
• USDA
• EPA
• Smithsonian Institute
• Department of the Interior
• Department of Commerce

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SNOMED's taxonomy of living organisms presently
consists of

• Linnean taxonomic terms (Canis familiaris)
• Common names for organisms (Dog)
• Non-taxonomic information
• Use and Circumstances
• Laboratory fur-bearing animal
• Pathogenicity
• Parasite, pyogenic bacterium
• Life cycle stage of organisms
• Worm eggs

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Common names as FSNswhy is this a problem?

• Some organisms have many common names
• Butorides virescens green heron, green-backed
  heron, little green heron, crab-catcher,
  fly-up-the-creek, green bittern, poke, shitepoke,
  skeow, skow, and swamp squaggin
• May be impossible to verify what organism is
  meant
• Ex Comte de Paris star frontlet (organism) ???
• A single common name may refer to more than one
  species
• Ex Yellowhammer (organism) MAY BE A Emberiza
  citrinella, MAY BE A Colaptes auratus

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Non-taxonomic terms in a taxonomic hierarchywhy
is this a problem?

• In an ISA hierarchy, the relationships are
  "defining," that is, a subtype is always and
  necessarily a "kind of" its parent
• The present interpolation of non-taxonomic terms
  in a taxonomic hierarchy violates this
  convention, as these terms are often
  context-dependent rather than defining. An
  elephant may be a domestic animal in India a dog
  may be a food animal in Korea
• Question Is a canary a Wild bird--chordate or
  a Domestic fowl?
• Answer Neither. It is Serinus canaria

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Work in progress

• Extending and correcting SNOMEDs taxonomic
  coverage of birds and mammals
• Retiring common names as FSNs and referring them
  as synonyms to the appropriate scientific names

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Proposed further changes

• To represent contextual information about living
  organisms outside the taxonomic hierarchy
• Contexts of domesticity (domestic, feral, wild)
• Contexts of use (food, laboratory, companion,
  service, breeding, etc)
• Contexts of life stage (oocyst, larva, spore,
  trophozooite, etc)
• Contexts of medical significance (parasite,
  renotrophic organism, pathogen)???

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Life, qualified?

• Qualifier values offer one possible means to
  convey non-taxonomic information about living
  organisms, just as qualifiers such as onsets,
  severities, or courses can be used to describe a
  disease

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An unqualified mink

• Mink
• ISA Domestic animal species, non-primate
  (organism)

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A qualified mink

• Mustela vison (syn. Mink)
• ISA Genus Mustela
• Qualifier values
• Context of use
• Fur-bearing animal
• Laboratory animal
• Etc.
• Context of domestication
• Wild
• Domestic
• Feral

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What about infectious agents?

• The taxonomy of parasites, bacteria and other
  potentially pathogenic microorganisms is also a
  mixture of scientific names, common names, and
  contextual information
• Attempting to convey contexts of pathogenicity
  creates errors in logic
• Ex Helminth ISA Parasite in SNOMED-but most
  helminths are not parasitic
• Ex Fungus ISA Infectious agent in SNOMEDbut
  most fungi are not infectious